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1. Development of MHz X-ray phase contrast imaging at the European XFEL

Author

Jayanath C. P. Koliyadu, Daniel Moško, Eleni Myrto Asimakopoulou, Valerio Bellucci, Šarlota Birnšteinová, Richard Bean, Romain Letrun, Chan Kim, Henry Kirkwood, Gabriele Giovanetti, Nerea Jardon, Janusz Szuba, Trey Guest, Andreas Koch, Jan Grünert, Peter Szeles, Pablo Villanueva-Perez, Fabian Reuter, Claus-Dieter Ohl, Mike Andreas Noack, Francisco Garcia-Moreno, Zuzana Kuglerová-Valdová, Libor Juha, Martin Nikl, Wataru Yashiro, Hitoshi Soyama, Daniel Eakins, Alexander M. Korsunsky, Jozef Uličný, Alke Meents, Henry N. Chapman, Adrian P. Mancuso, Tokushi Sato, and Patrik Vagovič

Subjects
megahertz sampling, x-ray phase contrast imaging, pulse-resolved imaging, indirect mhz x-ray detector, european xfel, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798, Crystallography, QD901-999
Abstract

We report on recent developments that enable megahertz hard X-ray phase contrast imaging (MHz XPCI) experiments at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of the European XFEL facility (EuXFEL). We describe the technical implementation of the key components, including an MHz fast camera and a modular indirect X-ray microscope system based on fast scintillators coupled through a high-resolution optical microscope, which enable full-field X-ray microscopy with phase contrast of fast and irreversible phenomena. The image quality for MHz XPCI data showed significant improvement compared with a pilot demonstration of the technique using parallel beam illumination, which also allows access to up to 24 keV photon energies at the SPB/SFX instrument of the EuXFEL. With these developments, MHz XPCI was implemented as a new method offered for a broad user community (academic and industrial) and is accessible via standard user proposals. Furthermore, intra-train pulse diagnostics with a high few-micrometre spatial resolution and recording up to 128 images of consecutive pulses in a train at up to 1.1 MHz repetition rate is available upstream of the instrument. Together with the diagnostic camera upstream of the instrument and the MHz XPCI setup at the SPB/SFX instrument, simultaneous two-plane measurements for future beam studies and feedback for machine parameter tuning are now possible.

Published
2025
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2. Megahertz-rate ultrafast X-ray scattering and holographic imaging at the European XFEL

Author

Nanna Zhou Hagström, Michael Schneider, Nico Kerber, Alexander Yaroslavtsev, Erick Burgos Parra, Marijan Beg, Martin Lang, Christian M. Günther, Boris Seng, Fabian Kammerbauer, Horia Popescu, Matteo Pancaldi, Kumar Neeraj, Debanjan Polley, Rahul Jangid, Stjepan B. Hrkac, Sheena K. K. Patel, Sergei Ovcharenko, Diego Turenne, Dmitriy Ksenzov, Christine Boeglin, Marina Baidakova, Clemens von Korff Schmising, Martin Borchert, Boris Vodungbo, Kai Chen, Chen Luo, Florin Radu, Leonard Müller, Miriam Martínez Flórez, André Philippi-Kobs, Matthias Riepp, Wojciech Roseker, Gerhard Grübel, Robert Carley, Justine Schlappa, Benjamin E. Van Kuiken, Rafael Gort, Laurent Mercadier, Naman Agarwal, Loïc Le Guyader, Giuseppe Mercurio, Martin Teichmann, Jan Torben Delitz, Alexander Reich, Carsten Broers, David Hickin, Carsten Deiter, James Moore, Dimitrios Rompotis, Jinxiong Wang, Daniel Kane, Sandhya Venkatesan, Joachim Meier, Florent Pallas, Tomasz Jezynski, Maximilian Lederer, Djelloul Boukhelef, Janusz Szuba, Krzysztof Wrona, Steffen Hauf, Jun Zhu, Martin Bergemann, Ebad Kamil, Thomas Kluyver, Robert Rosca, Michał Spirzewski, Markus Kuster, Monica Turcato, David Lomidze, Andrey Samartsev, Jan Engelke, Matteo Porro, Stefano Maffessanti, Karsten Hansen, Florian Erdinger, Peter Fischer, Carlo Fiorini, Andrea Castoldi, Massimo Manghisoni, Cornelia Beatrix Wunderer, Eric E. Fullerton, Oleg G. Shpyrko, Christian Gutt, Cecilia Sanchez-Hanke, Hermann A. Dürr, Ezio Iacocca, Hans T. Nembach, Mark W. Keller, Justin M. Shaw, Thomas J. Silva, Roopali Kukreja, Hans Fangohr, Stefan Eisebitt, Mathias Kläui, Nicolas Jaouen, Andreas Scherz, Stefano Bonetti, and Emmanuelle Jal

Subjects
xfel, holography, magnetic x-ray scattering, soft x-rays, ultrafast x-ray imaging, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798, Crystallography, QD901-999
Abstract

The advent of X-ray free-electron lasers (XFELs) has revolutionized fundamental science, from atomic to condensed matter physics, from chemistry to biology, giving researchers access to X-rays with unprecedented brightness, coherence and pulse duration. All XFEL facilities built until recently provided X-ray pulses at a relatively low repetition rate, with limited data statistics. Here, results from the first megahertz-repetition-rate X-ray scattering experiments at the Spectroscopy and Coherent Scattering (SCS) instrument of the European XFEL are presented. The experimental capabilities that the SCS instrument offers, resulting from the operation at megahertz repetition rates and the availability of the novel DSSC 2D imaging detector, are illustrated. Time-resolved magnetic X-ray scattering and holographic imaging experiments in solid state samples were chosen as representative, providing an ideal test-bed for operation at megahertz rates. Our results are relevant and applicable to any other non-destructive XFEL experiments in the soft X-ray range.

Published
2022
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3. Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers

Author

Susannah Holmes, Henry J. Kirkwood, Richard Bean, Klaus Giewekemeyer, Andrew V. Martin, Marjan Hadian-Jazi, Max O. Wiedorn, Dominik Oberthür, Hugh Marman, Luigi Adriano, Nasser Al-Qudami, Saša Bajt, Imrich Barák, Sadia Bari, Johan Bielecki, Sandor Brockhauser, Mathew A. Coleman, Francisco Cruz-Mazo, Cyril Danilevski, Katerina Dörner, Alfonso M. Gañán-Calvo, Rita Graceffa, Hans Fanghor, Michael Heymann, Matthias Frank, Alexander Kaukher, Yoonhee Kim, Bostjan Kobe, Juraj Knoška, Torsten Laurus, Romain Letrun, Luis Maia, Marc Messerschmidt, Markus Metz, Thomas Michelat, Grant Mills, Serguei Molodtsov, Diana C. F. Monteiro, Andrew J. Morgan, Astrid Münnich, Gisel E. Peña Murillo, Gianpietro Previtali, Adam Round, Tokushi Sato, Robin Schubert, Joachim Schulz, Megan Shelby, Carolin Seuring, Jonas A. Sellberg, Marcin Sikorski, Alessandro Silenzi, Stephan Stern, Jola Sztuk-Dambietz, Janusz Szuba, Martin Trebbin, Patrick Vagovic, Thomas Ve, Britta Weinhausen, Krzysztof Wrona, Paul Lourdu Xavier, Chen Xu, Oleksandr Yefanov, Keith A. Nugent, Henry N. Chapman, Adrian P. Mancuso, Anton Barty, Brian Abbey, and Connie Darmanin

Subjects
Science
Abstract

Free-electron lasers are capable of high repetition rates and it is assumed that protein crystals often do not survive the first X-ray pulse. Here the authors address these issues with a demonstration of multi-hit serial crystallography in which multiple FEL pulses interact with the sample without destroying it.

Published
2022
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4. Membrane protein megahertz crystallography at the European XFEL

Author

Chris Gisriel, Jesse Coe, Romain Letrun, Oleksandr M. Yefanov, Cesar Luna-Chavez, Natasha E. Stander, Stella Lisova, Valerio Mariani, Manuela Kuhn, Steve Aplin, Thomas D. Grant, Katerina Dörner, Tokushi Sato, Austin Echelmeier, Jorvani Cruz Villarreal, Mark S. Hunter, Max O. Wiedorn, Juraj Knoska, Victoria Mazalova, Shatabdi Roy-Chowdhury, Jay-How Yang, Alex Jones, Richard Bean, Johan Bielecki, Yoonhee Kim, Grant Mills, Britta Weinhausen, Jose D. Meza, Nasser Al-Qudami, Saša Bajt, Gerrit Brehm, Sabine Botha, Djelloul Boukhelef, Sandor Brockhauser, Barry D. Bruce, Matthew A. Coleman, Cyril Danilevski, Erin Discianno, Zachary Dobson, Hans Fangohr, Jose M. Martin-Garcia, Yaroslav Gevorkov, Steffen Hauf, Ahmad Hosseinizadeh, Friederike Januschek, Gihan K. Ketawala, Christopher Kupitz, Luis Maia, Maurizio Manetti, Marc Messerschmidt, Thomas Michelat, Jyotirmoy Mondal, Abbas Ourmazd, Gianpietro Previtali, Iosifina Sarrou, Silvan Schön, Peter Schwander, Megan L. Shelby, Alessandro Silenzi, Jolanta Sztuk-Dambietz, Janusz Szuba, Monica Turcato, Thomas A. White, Krzysztof Wrona, Chen Xu, Mohamed H. Abdellatif, James D. Zook, John C. H. Spence, Henry N. Chapman, Anton Barty, Richard A. Kirian, Matthias Frank, Alexandra Ros, Marius Schmidt, Raimund Fromme, Adrian P. Mancuso, Petra Fromme, and Nadia A. Zatsepin

Subjects
Science
Abstract

The European X-ray free-electron laser (EuXFEL) in Hamburg is the first XFEL with a megahertz repetition rate. Here the authors present the 2.9 Å structure of the large membrane protein complex Photosystem I from T. elongatus that was determined at the EuXFEL.

Published
2019
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5. Megahertz serial crystallography

Author

Max O. Wiedorn, Dominik Oberthür, Richard Bean, Robin Schubert, Nadine Werner, Brian Abbey, Martin Aepfelbacher, Luigi Adriano, Aschkan Allahgholi, Nasser Al-Qudami, Jakob Andreasson, Steve Aplin, Salah Awel, Kartik Ayyer, Saša Bajt, Imrich Barák, Sadia Bari, Johan Bielecki, Sabine Botha, Djelloul Boukhelef, Wolfgang Brehm, Sandor Brockhauser, Igor Cheviakov, Matthew A. Coleman, Francisco Cruz-Mazo, Cyril Danilevski, Connie Darmanin, R. Bruce Doak, Martin Domaracky, Katerina Dörner, Yang Du, Hans Fangohr, Holger Fleckenstein, Matthias Frank, Petra Fromme, Alfonso M. Gañán-Calvo, Yaroslav Gevorkov, Klaus Giewekemeyer, Helen Mary Ginn, Heinz Graafsma, Rita Graceffa, Dominic Greiffenberg, Lars Gumprecht, Peter Göttlicher, Janos Hajdu, Steffen Hauf, Michael Heymann, Susannah Holmes, Daniel A. Horke, Mark S. Hunter, Siegfried Imlau, Alexander Kaukher, Yoonhee Kim, Alexander Klyuev, Juraj Knoška, Bostjan Kobe, Manuela Kuhn, Christopher Kupitz, Jochen Küpper, Janine Mia Lahey-Rudolph, Torsten Laurus, Karoline Le Cong, Romain Letrun, P. Lourdu Xavier, Luis Maia, Filipe R. N. C. Maia, Valerio Mariani, Marc Messerschmidt, Markus Metz, Davide Mezza, Thomas Michelat, Grant Mills, Diana C. F. Monteiro, Andrew Morgan, Kerstin Mühlig, Anna Munke, Astrid Münnich, Julia Nette, Keith A. Nugent, Theresa Nuguid, Allen M. Orville, Suraj Pandey, Gisel Pena, Pablo Villanueva-Perez, Jennifer Poehlsen, Gianpietro Previtali, Lars Redecke, Winnie Maria Riekehr, Holger Rohde, Adam Round, Tatiana Safenreiter, Iosifina Sarrou, Tokushi Sato, Marius Schmidt, Bernd Schmitt, Robert Schönherr, Joachim Schulz, Jonas A. Sellberg, M. Marvin Seibert, Carolin Seuring, Megan L. Shelby, Robert L. Shoeman, Marcin Sikorski, Alessandro Silenzi, Claudiu A. Stan, Xintian Shi, Stephan Stern, Jola Sztuk-Dambietz, Janusz Szuba, Aleksandra Tolstikova, Martin Trebbin, Ulrich Trunk, Patrik Vagovic, Thomas Ve, Britta Weinhausen, Thomas A. White, Krzysztof Wrona, Chen Xu, Oleksandr Yefanov, Nadia Zatsepin, Jiaguo Zhang, Markus Perbandt, Adrian P. Mancuso, Christian Betzel, Henry Chapman, and Anton Barty

Subjects
Science
Abstract

The new European X-Ray Free-Electron Laser (EuXFEL) is the first XFEL that generates X-ray pulses with a megahertz inter-pulse spacing. Here the authors demonstrate that high-quality and damage-free protein structures can be obtained with the currently available 1.1 MHz repetition rate pulses using lysozyme as a test case and furthermore present a β-lactamase structure.

Published
2018
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6. Megahertz data collection from protein microcrystals at an X-ray free-electron laser

Author

Marie Luise Grünbein, Johan Bielecki, Alexander Gorel, Miriam Stricker, Richard Bean, Marco Cammarata, Katerina Dörner, Lars Fröhlich, Elisabeth Hartmann, Steffen Hauf, Mario Hilpert, Yoonhee Kim, Marco Kloos, Romain Letrun, Marc Messerschmidt, Grant Mills, Gabriela Nass Kovacs, Marco Ramilli, Christopher M. Roome, Tokushi Sato, Matthias Scholz, Michel Sliwa, Jolanta Sztuk-Dambietz, Martin Weik, Britta Weinhausen, Nasser Al-Qudami, Djelloul Boukhelef, Sandor Brockhauser, Wajid Ehsan, Moritz Emons, Sergey Esenov, Hans Fangohr, Alexander Kaukher, Thomas Kluyver, Max Lederer, Luis Maia, Maurizio Manetti, Thomas Michelat, Astrid Münnich, Florent Pallas, Guido Palmer, Gianpietro Previtali, Natascha Raab, Alessandro Silenzi, Janusz Szuba, Sandhya Venkatesan, Krzysztof Wrona, Jun Zhu, R. Bruce Doak, Robert L. Shoeman, Lutz Foucar, Jacques-Philippe Colletier, Adrian P. Mancuso, Thomas R. M. Barends, Claudiu A. Stan, and Ilme Schlichting

Subjects
Science
Abstract

The European X-ray free-electron laser (EuXFEL) in Hamburg is the first megahertz (MHz) repetition rate XFEL. Here the authors use lysozyme crystals and microcrystals from jack bean proteins and demonstrate that damage-free high quality data can be collected at a MHz repetition rate.

Published
2018
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7. Author Correction: Membrane protein megahertz crystallography at the European XFEL

Author

Chris Gisriel, Jesse Coe, Romain Letrun, Oleksandr M. Yefanov, Cesar Luna-Chavez, Natasha E. Stander, Stella Lisova, Valerio Mariani, Manuela Kuhn, Steve Aplin, Thomas D. Grant, Katerina Dörner, Tokushi Sato, Austin Echelmeier, Jorvani Cruz Villarreal, Mark S. Hunter, Max O. Wiedorn, Juraj Knoska, Victoria Mazalova, Shatabdi Roy-Chowdhury, Jay-How Yang, Alex Jones, Richard Bean, Johan Bielecki, Yoonhee Kim, Grant Mills, Britta Weinhausen, Jose D. Meza, Nasser Al-Qudami, Saša Bajt, Gerrit Brehm, Sabine Botha, Djelloul Boukhelef, Sandor Brockhauser, Barry D. Bruce, Matthew A. Coleman, Cyril Danilevski, Erin Discianno, Zachary Dobson, Hans Fangohr, Jose M. Martin-Garcia, Yaroslav Gevorkov, Steffen Hauf, Ahmad Hosseinizadeh, Friederike Januschek, Gihan K. Ketawala, Christopher Kupitz, Luis Maia, Maurizio Manetti, Marc Messerschmidt, Thomas Michelat, Jyotirmoy Mondal, Abbas Ourmazd, Gianpietro Previtali, Iosifina Sarrou, Silvan Schön, Peter Schwander, Megan L. Shelby, Alessandro Silenzi, Jolanta Sztuk-Dambietz, Janusz Szuba, Monica Turcato, Thomas A. White, Krzysztof Wrona, Chen Xu, Mohamed H. Abdellatif, James D. Zook, John C. H. Spence, Henry N. Chapman, Anton Barty, Richard A. Kirian, Matthias Frank, Alexandra Ros, Marius Schmidt, Raimund Fromme, Adrian P. Mancuso, Petra Fromme, and Nadia A. Zatsepin

Subjects
Science
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020
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12. Femtosecond timing synchronization at megahertz repetition rates for an x-ray free-electron laser

Author

Guido Palmer, Tokushi Sato, Andrea Parenti, Marc Planas, Tomasz Jezynski, Patrik Vagovic, Alessandro Silenzi, Adrian P. Mancuso, Jia Liu, Sebastian A. Schulz, Henry Kirkwood, Cedric M. S. Takem, Romain Letrun, Moritz Emons, Jost Mueller, Max Lederer, Jan Grünert, Henry N. Chapman, Holger Schlarb, Thomas Michelat, Janusz Szuba, Martin Bergemann, Gabriele Giovanetti, Yoonhee Kim, and Grant Mills

Subjects
Physics, Repetition (rhetorical device), business.industry, Free-electron laser, 02 engineering and technology, 021001 nanoscience & nanotechnology, Laser, 01 natural sciences, Atomic and Molecular Physics, and Optics, Electronic, Optical and Magnetic Materials, law.invention, 010309 optics, Optics, law, Temporal resolution, 0103 physical sciences, Femtosecond, Synchronization (computer science), Light beam, ddc:620, 0210 nano-technology, business, Jitter
Abstract

Optica 7(6), 716 - (2020). doi:10.1364/OPTICA.396728, A critical challenge of pump-probe experiments with x-ray free-electron lasers (XFELs) is accurate synchronization of x-ray and optical pulses. At the European XFEL we observed megahertz rate timing jitter of 24.0±12.4fs., Published by OSA, Washington, DC

Published
2020
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13. Membrane protein megahertz crystallography at the European XFEL

Author

Stella Lisova, Jolanta Sztuk-Dambietz, Peter Schwander, Juraj Knoska, Alessandro Silenzi, Natasha Stander, Y. Gevorkov, Oleksandr Yefanov, Saša Bajt, Johan Bielecki, Shatabdi Roy-Chowdhury, Jesse Coe, Cyril Danilevski, Nasser Al-Qudami, Marius Schmidt, Matthew A. Coleman, James Zook, Christopher J. Gisriel, Ahmad Hosseinizadeh, Anton Barty, Megan L. Shelby, Djelloul Boukhelef, Jose M. Martin-Garcia, Marc Messerschmidt, Jose D. Meza, Luis Maia, Henry N. Chapman, Katerina Dörner, Yoonhee Kim, Grant Mills, Mark S. Hunter, Krzysztof Wrona, Gerrit Brehm, Sandor Brockhauser, Erin Discianno, Silvan Schön, Abbas Ourmazd, Tokushi Sato, Christopher Kupitz, John C. H. Spence, Adrian P. Mancuso, Richard Bean, Iosifina Sarrou, Steffen Hauf, Hans Fangohr, Valerio Mariani, Gianpietro Previtali, Cesar Luna-Chavez, Thomas Michelat, Steve Aplin, Manuela Kuhn, Austin Echelmeier, Britta Weinhausen, Jorvani Cruz Villarreal, Thomas D. Grant, Janusz Szuba, Maurizio Manetti, Barry D. Bruce, Gihan K. Ketawala, Monica Turcato, Jay How Yang, Raimund Fromme, Mohamed H. Abdellatif, Petra Fromme, Sabine Botha, Max O. Wiedorn, Richard A. Kirian, Romain Letrun, Matthias Frank, Friederike Januschek, Alexandra Ros, Alex Jones, Jyotirmoy Mondal, Victoria Mazalova, Chen Xu, Thomas A. White, Zachary Dobson, and Nadia A. Zatsepin

Subjects
Models, Molecular, 0301 basic medicine, Thermosynechococcus, General Physics and Astronomy, 02 engineering and technology, Informatik [004], Cell size, law.invention, Models, law, lcsh:Science, Crystallography, Multidisciplinary, Nanocrystallography, 021001 nanoscience & nanotechnology, Membrane protein complex, Femtosecond, ddc:500, 0210 nano-technology, Structural biology, Materials science, Science, 1.1 Normal biological development and functioning, Static Electricity, Electrons, Rapid pulse, Cyanobacteria, Photosystem I, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Underpinning research, ddc:530, Author Correction, Physik [530], X-ray crystallography, Photosystem I Protein Complex, Lasers, X-Rays, Molecular, Membrane Proteins, European XFEL, General Chemistry, Laser, 030104 developmental biology, Membrane protein, lcsh:Q, Generic health relevance, ddc:004, Synchrotrons
Abstract

Nature Communications 10(1), 11 (2019). doi:10.1038/s41467-019-12955-3, The world’s first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs., Published by Nature Publishing Group UK, [London]

Published
2019
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14. MHz data collection of a microcrystalline mixture of different jack bean proteins

Author

Gabriela Nass Kovacs, Djelloul Boukhelef, Alexander Kaukher, Sandhya Venkatesan, Astrid Münnich, Michel Sliwa, Nasser Al-Qudami, Jolanta Sztuk-Dambietz, Sergey Esenov, Lutz Foucar, A. Gorel, Krzysztof Wrona, Janusz Szuba, Maurizio Manetti, Thomas Kluyver, Marco Cammarata, Jun Zhu, Johan Bielecki, Matthias Scholz, Marc Messerschmidt, Richard Bean, Gianpietro Previtali, Thomas Michelat, Sandor Brockhauser, Natascha Raab, M. Hilpert, Thomas R. M. Barends, Alessandro Silenzi, Katerina Dörner, Moritz Emons, Yoonhee Kim, Grant Mills, C.M. Roome, Luis Maia, Max Lederer, Jacques-Philippe Colletier, Wajid Ehsan, Steffen Hauf, Britta Weinhausen, Marco Ramilli, Marco Kloos, Elisabeth Hartmann, Romain Letrun, Claudiu A. Stan, Florent Pallas, Marie Luise Grünbein, R. Bruce Doak, Martin Weik, Lars Fröhlich, M. Stricker, Robert L. Shoeman, Guido Palmer, Tokushi Sato, Hans Fangohr, Ilme Schlichting, Adrian P. Mancuso, European XFEL GmbH (XFEL), European XFEL GmbH, Max Planck Institute for Medical Research [Heidelberg], Max-Planck-Gesellschaft, Institut de Physique de Rennes (IPR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Elettra Sincrotrone Trieste, National Science Foundation [Arlington] (NSF), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), KEK (High energy accelerator research organization), TOPTICA Photonics AG, Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), European Synchrotron Radiation Facility (ESRF), European Molecular Biology Laboratory [Grenoble] (EMBL), Institut de Microélectronique, Electromagnétisme et Photonique (IMEP), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS), NINGBO UNIVERSITY, Ningbo University (NBU), Department of Biomolecular Mechanisms, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Rutgers University [Newark], Rutgers University System (Rutgers), Deutsches Elektronen-Synchrotron, ANR-17-CE11-0018-01, Agence Nationale de la Recherche, European XFEL, ANR Grant, European XFEL - travel funding provided by the International Synchrotron Access Program (ISAP) managed by the Australian Synchrotron, part of ANSTO, and funded by the Australian Government, ANR Grant (BioXFEL) CEA, CNRS, Universit&amp, x00E9, Grenoble Alpes, startup funds from Rutgers University Newark, ANR-17-CE11-0018,X-in-vivo,Cristallisation in vivo: une nouvelle stratégie pour étudier la structure et la dynamique des protéines dans les lasers à électrons libres et les synchrotrons.(2017), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille Institut (CLIL), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Grenoble (INPG)-Université Joseph Fourier - Grenoble 1 (UJF)

Subjects
Statistics and Probability, Data Descriptor, 010504 meteorology & atmospheric sciences, Computer science, Library and Information Sciences, Crystallography, X-Ray, 01 natural sciences, Education, law.invention, 03 medical and health sciences, Optics, law, Concanavalin A, [CHIM]Chemical Sciences, lcsh:Science, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0105 earth and related environmental sciences, Plant Proteins, [PHYS]Physics [physics], 0303 health sciences, Data collection, business.industry, Nanocrystallography, Detector, Proteins, Frame rate, Laser, Sample (graphics), Urease, Computer Science Applications, Data set, Microcrystalline, Femtosecond, Enzyme mechanisms, lcsh:Q, ddc:500, Statistics, Probability and Uncertainty, business, Crystallization, Information Systems
Abstract

Scientific data 6(1), 18 (2019). doi:10.1038/s41597-019-0010-0, We provide a detailed description of a serial femtosecond crystallography (SFX) dataset collected at the European X-ray free-electron laser facility (EuXFEL). The EuXFEL is the first high repetition rate XFEL delivering MHz X-ray pulse trains at 10 Hz. The short spacing (, Published by Nature Publ. Group, London

Published
2019
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15. FAST-XPD: XFEL photon pulses database for modeling XFEL experiments

Author

Janusz Szuba, Krzysztof Wrona, Mikhail Yurkov, Evgeny Schneidmiller, Maurizio Manetti, Alexey Buzmakov, Liubov Samoylova, and Harald Sinn

Subjects
Physics, Photon, Database, Physics::Accelerator Physics, ddc:530, Radiation, computer.software_genre, computer
Abstract

13th International Conference on Synchrotron Radiation Instrumentation, SRI2018, Taipei, Taiwan, 10 Jun 2018 - 15 Jun 2018; AIP conference proceedings 2054(1), 030019 (2019). doi:10.1063/1.5084582, Knowledge of different properties of the radiation from X-ray FEL is very important for planning experiments. An understanding of such properties can come from start-to-end simulations of experiments: modern FEL simulation allows to reliably predict the output radiation pulses from X-ray FEL. We present a web a ccessible XFEL photon pulses simulation database showing data calculated with the FAST simulation framework., Published by AIP, Melville, NY

Published
2019
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16. Megahertz Data Collection from Protein Microcrystals at an X-Ray Free-Electron Laser

Author

Florent Pallas, Alexander Kaukher, Martin Weik, Richard Bean, Thomas Michelat, Nasser Al-Qudami, Natascha Raab, Guido Palmer, Yoonhee Kim, Grant Mills, M. Hilpert, Gianpietro Previtali, M. Stricker, Lars Fröhlich, Claudiu A. Stan, Tokushi Sato, Maurizio Manetti, Sergey Esenov, Gabriela Nass Kovacs, Thomas R. M. Barends, Katerina Dörner, Matthias Scholz, Marie Luise Grünbein, Jolanta Sztuk-Dambietz, Elisabeth Hartmann, Steffen Hauf, Robert L. Shoeman, A. Gorel, Britta Weinhausen, Janusz Szuba, Thomas Kluyver, Alessandro Silenzi, Astrid Münnich, Michel Sliwa, Djelloul Boukhelef, Marc Messerschmidt, Krzysztof Wrona, Sandhya Venkatesan, Moritz Emons, C.M. Roome, Jacques-Philippe Colletier, Wajid Ehsan, Marco Kloos, Marco Cammarata, Jun Zhu, Lutz Foucar, Luis Maia, Max Lederer, Hans Fangohr, Marco Ramilli, Johan Bielecki, Ilme Schlichting, Sandor Brockhauser, Adrian P. Mancuso, Romain Letrun, R. Bruce Doak, Max Planck Institute for Medical Research [Heidelberg], Max-Planck-Gesellschaft, European XFEL GmbH (XFEL), European XFEL GmbH, Institut de Physique de Rennes (IPR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Deutsches Elektronensynchrotron DESY, D-22607 Hamburg, Germany, Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille Institut (CLIL), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Rutgers University [Newark], Rutgers University System (Rutgers), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and ANR-17-CE11-0018,X-in-vivo,Cristallisation in vivo: une nouvelle stratégie pour étudier la structure et la dynamique des protéines dans les lasers à électrons libres et les synchrotrons.(2017)

Subjects
0301 basic medicine, Shock wave, Materials science, Science, General Physics and Astronomy, 02 engineering and technology, General Biochemistry, Genetics and Molecular Biology, Article, law.invention, 03 medical and health sciences, Optics, law, lcsh:Science, [PHYS]Physics [physics], Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Femtosecond pulse, business.industry, Free-electron laser, X-ray, General Chemistry, 021001 nanoscience & nanotechnology, Laser, Pulse (physics), 030104 developmental biology, Femtosecond, lcsh:Q, ddc:500, 0210 nano-technology, business, Beam (structure)
Abstract

Nature Communications 9(1), 3487 (2018). doi:10.1038/s41467-018-05953-4, X-ray free-electron lasers (XFELs) enable novel experiments because of their high peak brilliance and femtosecond pulse duration. However, non-superconducting XFELs offer repetition rates of only 10–120 Hz, placing significant demands on beam time and sample consumption. We describe serial femtosecond crystallography experiments performed at the European XFEL, the first MHz repetition rate XFEL, delivering 1.128 MHz X-ray pulse trains at 10 Hz. Given the short spacing between pulses, damage caused by shock waves launched by one XFEL pulse on sample probed by subsequent pulses is a concern. To investigate this issue, we collected data from lysozyme microcrystals, exposed to a ~15 μm XFEL beam. Under these conditions, data quality is independent of whether the first or subsequent pulses of the train were used for data collection. We also analyzed a mixture of microcrystals of jack bean proteins, from which the structure of native, magnesium-containing concanavalin A was determined., Published by Springer Nature, London

Published
2018
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17. Author Correction: Membrane protein megahertz crystallography at the European XFEL

Author

Ahmad Hosseinizadeh, Thomas A. White, Zachary Dobson, Friederike Januschek, Romain Letrun, Djelloul Boukhelef, Megan L. Shelby, Petra Fromme, Stella Lisova, Katerina Dörner, Sandor Brockhauser, Matthias Frank, Barry D. Bruce, Maurizio Manetti, Richard Bean, Krzysztof Wrona, Anton Barty, Yoonhee Kim, Gianpietro Previtali, Max O. Wiedorn, Grant Mills, Sabine Botha, Cyril Danilevski, Monica Turcato, Johan Bielecki, Jolanta Sztuk-Dambietz, Peter Schwander, Marius Schmidt, Steffen Hauf, Erin Discianno, Mark S. Hunter, Christopher J. Gisriel, Janusz Szuba, Britta Weinhausen, Saša Bajt, Jose D. Meza, Richard A. Kirian, Silvan Schön, Jose M. Martin-Garcia, Juraj Knoska, Luis Maia, Gihan K. Ketawala, Iosifina Sarrou, Nasser Al-Qudami, Hans Fangohr, Adrian P. Mancuso, Abbas Ourmazd, Raimund Fromme, Valerio Mariani, Gerrit Brehm, Jorvani Cruz Villarreal, Christopher Kupitz, Alexandra Ros, Manuela Kuhn, Steve Aplin, Shatabdi Roy-Chowdhury, Austin Echelmeier, Alessandro Silenzi, John C. H. Spence, Thomas D. Grant, Cesar Luna-Chavez, Thomas Michelat, Natasha Stander, Jay How Yang, Matthew A. Coleman, Mohamed H. Abdellatif, Chen Xu, Nadia A. Zatsepin, Alex Jones, Jyotirmoy Mondal, Victoria Mazalova, Y. Gevorkov, Jesse Coe, James Zook, Marc Messerschmidt, Henry N. Chapman, Oleksandr Yefanov, and Tokushi Sato

Subjects
Physics, 0303 health sciences, Multidisciplinary, Published Erratum, Science, General Physics and Astronomy, 02 engineering and technology, General Chemistry, 021001 nanoscience & nanotechnology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Crystallography, Membrane protein, lcsh:Q, 0210 nano-technology, lcsh:Science, 030304 developmental biology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020
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18. Detectors and Calibration Concept for the European XFEL

Author

Luis Maia, Djelloul Boukhelef, Steffen Hauf, Janusz Szuba, Krzysztof Wrona, Monica Turcato, Natascha Raab, J.-S. Dambietz, C. Youngman, Mattia Donato, and Markus Kuster

Subjects
Physics, Nuclear and High Energy Physics, Photon, business.industry, Detector, Free-electron laser, Atomic and Molecular Physics, and Optics, Linear particle accelerator, Optics, Bunches, Beamline, Calibration, Physics::Accelerator Physics, Spontaneous emission, business
Abstract

The European X-ray Free Electron Laser (XFEL.EU) is an international research facility presently under construction in the area of Hamburg, Germany, which will start its operation at the end of 2016 [1]. The superconducting linear accelerator of the facility will deliver electron bunches with an energy of up to 17.5 GeV, arranged in trains of typically 2700 bunches at a repetition rate of 4.5 MHz. Each train will be followed by a gap of 99.4 ms. Spatially coherent X-rays are generated from the electron bunches in a series of undulators based on the Self-Amplified Spontaneous Emission (SASE) process, in three photon beamlines extending over a length of up to 200 m. Each beamline serves two experiments with different scientific goals.

Published
2014
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19. New Object-Oriented PROGRES for Specifying the Conceptual Design Tool GraCAD

Author

Janusz Szuba

Subjects
ArchiCAD, Object-oriented programming, Graph rewriting, Wait-for graph, Theoretical computer science, General Computer Science, Computer science, Programming language, Functional requirement, computer.software_genre, Graph, Theoretical Computer Science, PROGRES, Conceptual Design, Conceptual design, Java collections framework, Graph (abstract data type), CAD, computer, Computer Science(all)
Abstract

This paper deals with the application of graph transformations for the specification of conceptual design tools. We show how the graph rewriting system PROGRES is used for specifying the graph part of the conceptual method for architects in which functional requirements of the building to be designed are elicited by means of graph structures. The consistency of the specified requirements and whether a design matches those requirements is verified with graph constraint checkers. We consider how the new object-oriented extensions of the PROGRES language, i.e. packages and node objects with redefinable methods can be used to achieve the required constraint monitoring and preserving functions in the form of graph checker objects. The prototype for our method, called GraCAD, is created with UPGRADE - the recently developed Java framework for developing visual applications based on a PROGRES specification, and the commercial system for architects ArchiCAD.

Published
2005
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21. On Graphs in Conceptual Engineering Design

Author

Andy Schürr, Janusz Szuba, and Agnieszka Ozimek

Subjects
Graph rewriting, Theoretical computer science, Conceptual design, Computer science, Programming language, Computer Aided Design, Use case, Functional requirement, Engineering design process, computer.software_genre, computer, Graph
Abstract

This paper deals with the subject of knowledge-based computer aided design. A novel method, giving additional support for conceptual design, is presented. Using this method, a designer first specifies the functional requirements and the structure of the object to be designed, based on use cases and function graphs. A prototype design is then derived from these requirements. Subsequently, the designer checks the fulfilment of certain consistency rules and engineering norms by the application of a constraint checker. This checker uses background knowledge stored in graph structures and the reasoning mechanism provided by the graph rewriting system PROGRES. An example of designing a swimming pool illustrates the proposed methodology.

Published
2004
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22. On Graph-Based Knowledge Representation in Design

Author

Adam Borkowski, Janusz Szuba, and Ewa Grabska

Subjects
Knowledge representation and reasoning, Commonsense knowledge, Computer science, business.industry, MultiNet, Procedural knowledge, computer.software_genre, Body of knowledge, Knowledge-based systems, Knowledge extraction, Domain knowledge, Artificial intelligence, business, computer, Natural language processing
Published
2002
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23. Graph Visualisation in ArchiCAD

Author

Janusz Szuba, Adam Borkowski, and Ewa Grabska

Subjects
Engineering drawing, Grammar, Graph drawing, Computer science, media_common.quotation_subject, Computer Aided Design, Graph (abstract data type), Architecture, computer.software_genre, computer, media_common
Abstract

This paper deals with computer aided design in architecture. A two-phase representation of objects is used that separates the definition of structure from the interpretation. It is shown how to integrate such a graph-based representation with the commercial ArchiCAD system used by many architects. Preliminary results reported in this paper indicate that it is possible to augment ArchiCAD by a graph grammar-based tool that would allow the designer to generate alternative solutions and to evaluate them.

Published
2000
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